[gmx-users] xtc file

Moeed lecielll at googlemail.com
Sun May 23 05:26:21 CEST 2010


Dear experts,

I am trying to exclude all nonbonded interaction on hexane molecule.


1-For the md -rerun command I do not know how to get the input XTC file. the
program is expecting rerun.xtc

mdrun -rerun -*x breakdown.xtc* -s Hexane-Stack125_md.tpr *-o
ORIGINAL-Trajectory-NOexcl.tpr* -c Hexane-Stack125_after_md -v >&
output.mdrun_m

2-Can you please check exclsusions directive in top file. I have used also
nrexcl 5 in molecule top. does this make sense given that I have defined all
the possible exclusions in 19 lines.




********************grompp em :

*checking input for internal consistency...
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 5 bonded neighbours molecule type 'Hexane'
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
Making dummy/rest group for T-Coupling containing 2500 elements
Making dummy/rest group for Acceleration containing 2500 elements
Making dummy/rest group for Freeze containing 2500 elements
Making dummy/rest group for Energy Mon. containing 2500 elements
Making dummy/rest group for VCM containing 2500 elements
Number of degrees of freedom in T-Coupling group rest is 5122.00
Making dummy/rest group for User1 containing 2500 elements
Making dummy/rest group for User2 containing 2500 elements
Making dummy/rest group for XTC containing 2500 elements
Making dummy/rest group for Or. Res. Fit containing 2500 elements
Making dummy/rest group for QMMM containing 2500 elements
T-Coupling       has 1 element(s): rest
Energy Mon.      has 1 element(s): rest
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
QMMM             has 1 element(s): rest
Checking consistency between energy and charge groups...

NOTE 1 [file em.mdp, line unknown]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.


writing run input file...

There was 1 note

Back Off! I just backed up Hexane-Stack125_em.tpr to
./#Hexane-Stack125_em.tpr.4#

gcq#320: "Do You Have Sex Maniacs or Schizophrenics or Astrophysicists in
Your Family?" (Gogol Bordello)

                         :-)  G  R  O  M  A  C  S  (-:

        Getting the Right Output Means no Artefacts in Calculating Stuff

                            :-)  VERSION 4.0.7  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2008, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                      :-)  grompp (double precision)  (-:

processing topology...
turning all bonds into constraints...
Analysing residue names:
There are:   125      OTHER residues
There are:     0    PROTEIN residues
There are:     0        DNA residues
Analysing Other...
This run will generate roughly 1 Mb of data

********************************************************************output
md_em:


teepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =          200
Step=    0, Dmax= 1.0e-02 nm, Epot= -2.41657e+03 Fmax= 1.96636e+02, atom=
1189

writing lowest energy coordinates.

Back Off! I just backed up Hexane-Stack125_b4pr.gro to
./#Hexane-Stack125_b4pr.gro.4#

Steepest Descents converged to Fmax < 1000 in 1 steps
Potential Energy  = -2.41656779590808e+03
Maximum force     =  1.96635853696765e+02 on atom 1189
Norm of force     =  1.37247833599652e+02
******************************************************************************************************out
put grompp md

Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaa.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaanb.itp
Opening library file /chem_soft/gromacs/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 5 bonded neighbours molecule type 'Hexane'
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Opening library file /chem_soft/gromacs/share/gromacs/top/aminoacids.dat
Making dummy/rest group for Acceleration containing 2500 elements
Making dummy/rest group for Freeze containing 2500 elements
Making dummy/rest group for Energy Mon. containing 2500 elements
Making dummy/rest group for VCM containing 2500 elements
Number of degrees of freedom in T-Coupling group HEX is 5122.00
Making dummy/rest group for User1 containing 2500 elements
Making dummy/rest group for User2 containing 2500 elements
Making dummy/rest group for XTC containing 2500 elements
Making dummy/rest group for Or. Res. Fit containing 2500 elements
Making dummy/rest group for QMMM containing 2500 elements
T-Coupling       has 1 element(s): HEX
Energy Mon.      has 1 element(s): rest
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
QMMM             has 1 element(s): rest
Checking consistency between energy and charge groups...
Estimate for the relative computational load of the PME mesh part: 0.13
writing run input file...

There was 1 note

Back Off! I just backed up Hexane-Stack125_md.tpr to
./#Hexane-Stack125_md.tpr.1#

gcq#190: "Load Up Your Rubber Bullets" (10 CC)

                         :-)  G  R  O  M  A  C  S  (-:

                Gravel Rubs Often Many Awfully Cauterized Sores

                            :-)  VERSION 4.0.7  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2008, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                      :-)  grompp (double precision)  (-:

processing topology...
turning all bonds into constraints...
Analysing residue names:
There are:   125      OTHER residues
There are:     0    PROTEIN residues
There are:     0        DNA residues
Analysing Other...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 42x21x21, spacing 0.119 0.119 0.119
This run will generate roughly 65 Mb of data
***********************************************************************











; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Hexane              5

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass
typeB    chargeB      massB
     1   opls_157      1    HEX     C1      1      -0.18     12.011   ; qtot
-0.18
     2   opls_140      1    HEX    H11      1       0.06      1.008   ; qtot
-0.12
     3   opls_140      1    HEX    H12      1       0.06      1.008   ; qtot
-0.06
     4   opls_140      1    HEX    H13      1       0.06      1.008   ; qtot
0
     5   opls_158      1    HEX     C2      2      -0.12     12.011   ; qtot
-0.12
     6   opls_140      1    HEX    H21      2       0.06      1.008   ; qtot
-0.06
     7   opls_140      1    HEX    H22      2       0.06      1.008   ; qtot
0
     8   opls_158      1    HEX     C3      3      -0.12     12.011   ; qtot
-0.12
     9   opls_140      1    HEX    H31      3       0.06      1.008   ; qtot
-0.06
    10   opls_140      1    HEX    H32      3       0.06      1.008   ; qtot
0
    11   opls_158      1    HEX     C4      4      -0.12     12.011   ; qtot
-0.12
    12   opls_140      1    HEX    H41      4       0.06      1.008   ; qtot
-0.06
    13   opls_140      1    HEX    H42      4       0.06      1.008   ; qtot
0
    14   opls_158      1    HEX     C5      5      -0.12     12.011   ; qtot
-0.12
    15   opls_140      1    HEX    H51      5       0.06      1.008   ; qtot
-0.06
    16   opls_140      1    HEX    H52      5       0.06      1.008   ; qtot
0
    17   opls_157      1    HEX     C6      6      -0.18     12.011   ; qtot
-0.18
    18   opls_140      1    HEX    H61      6       0.06      1.008   ; qtot
-0.12
    19   opls_140      1    HEX    H62      6       0.06      1.008   ; qtot
-0.06
    20   opls_140      1    HEX    H63      6       0.06      1.008   ; qtot
0

[ exclusions ]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
7 8 9 10 11 12 13 14 15 16 17 18 19 20
8 9 10 11 12 13 14 15 16 17 18 19 20
9 10 11 12 13 14 15 16 17 18 19 20
10 11 12 13 14 15 16 17 18 19 20
11 12 13 14 15 16 17 18 19 20
12 13 14 15 16 17 18 19 20
13 14 15 16 17 18 19 20
14 15 16 17 18 19 20
15 16 17 18 19 20
16 17 18 19 20
17 18 19 20
18 19 20
19 20

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1
    1     3     1
    1     4     1
    1     5     1
    5     6     1
    5     7     1
    5     8     1
    8     9     1
    8    10     1
    8    11     1
   11    12     1
   11    13     1
   11    14     1
   14    15     1
   14    16     1
   14    17     1
   17    18     1
   17    19     1
   17    20     1

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     9     1
    1    10     1
    1    11     1
    2     6     1
    2     7     1
    2     8     1
    3     6     1
    3     7     1
    3     8     1
    4     6     1
    4     7     1
    4     8     1
    5    12     1
    5    13     1
    5    14     1
    6     9     1
    6    10     1
    6    11     1
    7     9     1
    7    10     1
    7    11     1
    8    15     1
    8    16     1
    8    17     1
    9    12     1
    9    13     1
    9    14     1
   10    12     1
   10    13     1
   10    14     1
   11    18     1
   11    19     1
   11    20     1
   12    15     1
   12    16     1
   12    17     1
   13    15     1
   13    16     1
   13    17     1
   15    18     1
   15    19     1
   15    20     1
   16    18     1
   16    19     1
   16    20     1

[ angles ]
;  ai    aj    ak funct            c0            c1            c2
c3
    2     1     3     1
    2     1     4     1
    2     1     5     1
    3     1     4     1
    3     1     5     1
    4     1     5     1
    1     5     6     1
    1     5     7     1
    1     5     8     1
    6     5     7     1
    6     5     8     1
    7     5     8     1
    5     8     9     1
    5     8    10     1
    5     8    11     1
    9     8    10     1
    9     8    11     1
   10     8    11     1
    8    11    12     1
    8    11    13     1
    8    11    14     1
   12    11    13     1
   12    11    14     1
   13    11    14     1
   11    14    15     1
   11    14    16     1
   11    14    17     1
   15    14    16     1
   15    14    17     1
   16    14    17     1
   14    17    18     1
   14    17    19     1
   14    17    20     1
   18    17    19     1
   18    17    20     1
   19    17    20     1

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1
c2            c3            c4            c5
    2     1     5     6     3
    2     1     5     7     3
    2     1     5     8     3
    3     1     5     6     3
    3     1     5     7     3
    3     1     5     8     3
    4     1     5     6     3
    4     1     5     7     3
    4     1     5     8     3
    1     5     8     9     3
    1     5     8    10     3
    1     5     8    11     3
    6     5     8     9     3
    6     5     8    10     3
    6     5     8    11     3
    7     5     8     9     3
    7     5     8    10     3
    7     5     8    11     3
    5     8    11    12     3
    5     8    11    13     3
    5     8    11    14     3
    9     8    11    12     3
    9     8    11    13     3
    9     8    11    14     3
   10     8    11    12     3
   10     8    11    13     3
   10     8    11    14     3
    8    11    14    15     3
    8    11    14    16     3
    8    11    14    17     3
   12    11    14    15     3
   12    11    14    16     3
   12    11    14    17     3
   13    11    14    15     3
   13    11    14    16     3
   13    11    14    17     3
   11    14    17    18     3
   11    14    17    19     3
   11    14    17    20     3
   15    14    17    18     3
   15    14    17    19     3
   15    14    17    20     3
   16    14    17    18     3
   16    14    17    19     3
   16    14    17    20     3

; Include Position restraint file
;#ifdef POSRES
;#include "posre.itp"
;#endif

; Include water topology
;#include "spc.itp"

;#ifdef POSRES_WATER
; Position restraint for each water oxygen
;[ position_restraints ]
;  i funct       fcx        fcy        fcz
 ;  1    1       1000       1000       1000
;#endif

; Include generic topology for ions
;#include "ions.itp"

[ system ]
; Name
Hexane

[ molecules ]
; Compound        #mols
Hexane              125
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